Wednesday, August 31, 2011

Linux Runs Computational Neuroscience

Test Tubes

What OS is actually used in computational neuroscience? A recent paper in Frontiers in Neuroinformatics (let's hear it for Open Access!) has looked at this.

There's plenty of data there, but the main finding is that the most used system is Linux. Most researchers in the field use more than one OS, but Linux is the most common system, used by more than two-thirds of respondents, with Windows in second place with half and OSX third with a quarter1. Some people use Linux as their primary OS while others use it in a virtual machine or logged in to a remote machine somewhere else. Of course, many, even most people use more than one system.

One reason for the popularity of Linux is that many computational research tools are developed primarily for Linux and Unix; another one is that clusters and supercomputers mostly run Linux today. If you need to run your model or computation on a larger cluster you will need to use Linux in one form or another. But it's not simply a matter of necessity; the paper finds that satisfaction is also highest for Linux. Windows is most likely to be used specifically to access Word, Outlook or other specific software that only runs on Windows.

Now, the paper is based on an online survey and a self-selected sample of respondents; this is problematic at best. But it does fit with my own anecdotal experience. At OCNC I saw some people that primarily used Linux, but many more dual-booted Linux and another OS, or combined more than one OS using virtual machines. I often see similar setups at conferences and meetings as well.

Virtual machines have long been used on big servers and mainframes, but are fairly recent in the desktop world. A virtual machine — a VM — is a piece of software that emulates a real computer. You can install an operating system and applications in it and the OS will think it has direct access to the real hardware. In reality the virtual machine runs as an application in a host operating system, and tightly controls the access to the real system.

A VM is extremely convenient. You can start and stop the system it hosts at any time; you can save the entire system state into a (large) file on disk and go back to that saved image whenever you want, or copy that image to other computers to run there. It lets you create a specific software environment guaranteed to be the same every time you use it. Modern PCs lets a VM give out controlled access to the real hardware so there is not much speed reduction.

You can use a hosted Ubuntu Linux system for your software development and data analysis, use a remote cluster for your actual simulations, and the desktop OS you're already familiar with for email and web surfing. Or run Linux or OSX as your primary system, then a copy of Windows in a VM to access legacy Windows-only applications. Or run a second copy of your system in a VM, to make sure the environment is identical every time you run a simulation.
The major drawback of the virtual machine approach is really that each hosted OS really needs as much memory and disk space as if it was the only system on the computer. But modern laptops tend to have plenty of both, and for large simulations you're likely to use a remote cluster anyhow.

#1 This seemed a bit low to me at first. But this survey counts desktops and clusters as well, not just laptops, and OSX isn't nearly as prevalent in those areas as in portable computing. Also, Apple laptops have a very distinctive, uniform design; you end up with a positive bias where you remember seeing them but forget about all the anonymous, generic laptops that were really the majority at the meeting or the conference.

Monday, August 29, 2011

Noda new PM

The next political punching bag Finance Ministry handpuppet DPJ party president and Prime minister of Japan is Yoshihiko Noda. He is Finance minister, anti-Ozawa and has recently made some depressingly traditional waves by stating he does not believe the war criminals enshrined at Yasukuni were, in fact, war criminals at all.

The future is notoriously hard to predict, but we do know a few things: there is a regular DPJ party president election in September next year (exact date not fixed). The next lower house election must be held no later than the end of August 2013, but is likely to happen at any time during that spring or summer. There will be less than two years — more like a year and a half, and quite possibly less than that — between the regular party president election and the beginning of general election season and campaigning.

Barring a complete disaster1, the DPJ will not want to throw out their regularly elected leader and switch leaders again just a few months before the general election. This means that whoever wins the regular party president election next year is going to be2 their candidate in the general election in 2013.

If Noda is going to win that party president election next September, he will have to show basic electability. He and his cabinet will have to show decent public support numbers, and he must pull the DPJ up from the gutter and at least become more popular than the LDP. And to do that he'll need to show actual progress of some sort — progress on the economy, on the nuclear disaster mess, on rebuilding Tohoku, on the dysfunctional labour market, you name it. Many of these are problems that the central government has little leverage to do anything about, but all of the responsibility to resolve.

And he'll have to show progress in less than a year. With an opposition whose only tactic is to refuse any legislation offered by the government in order to discredit it. Leading a party where half the members want you out in favour of a champion of their own. And with a foreign policy in tatters before he even forms his cabinet, due to his incredibly boneheaded public defence of the war criminals at Yasukuni.

If he doesn't make it, he'll be out in a year. Everybody knows this, and nobody will risk their own career and throw their weight behind him unless he really seems to make progress and will prevail in next years leadership race. In practice he probably has a grace period of a month or less before the consensus verdict on him is in as either a future political powerhouse or a lame duck counting down the days until he follows Kan, Hatoyama, Aso, Fukuda and Abe into political footnotehood.

You may argue that his election is a momentous event in Japanese politics, that his policy ideas of tax increases and a grand coalition with the opposition will be implemented, and have lasting effect on today's problems and on the political climate. That he will stay on to ultimately contest the general election against the LDP. I would not say you are necessarily wrong. I would say the burden on proof is on you.

#1 Never underestimate the DPJ. They seem to have an unlimited capacity for political disaster even where you thought it could not possibly happen.

#2 "will hopefully be" is more realistic. See the previous footnote.

It's Monday Morning…

A few Monday morning notes, in no particular order:

  • I know paper reviews are simply reviewing your paper, not your work or yourself. That's what I do when I review other peoples papers after all. I know and appreciate that negative reviews are really helpful and we'll have a much better paper in the end. I know all this but I still take the criticism and the rejections personally.

    Most researchers I know are perennial — even pathological — optimists. You have to be, in order to deal with constant failure, uncertain funding and all the other stresses of research. I'm not an optimist at heart so I'm not emotionally cut out for this job.

  • My life would be measurably less stressful if it didn't currently include learning the standard kanji and several hundred obscure Japanese grammar points.

  • The election of the next DPJ leader, and thus Japanese prime minister is this afternoon. Get MTC's excellent take on the race here, and a voting analysis by sigma1 here.

    I'll write a few words about it once it's over, but I belong firmly in the "who wins doesn't really matter" camp, so I haven't found the energy or time to really cover this in any detail. MTC and the others do a much better job anyhow.

  • We'll be off to Sweden in another few weeks to see relatives. Central Sweden at the end of September promises to be cold, wet and dark. Right now I can't wait. And with any luck the worst of the summer here will be over by the time we come back.

    Really, we're almost ten million people here in Osaka ­— we could each pick up one piece of the city and move the whole thing to the north coast of Hokkaido. We'd have the same great city as now, but with cooler summers, no typhoons, skiing in the winter and the best seafood in the country!

Thursday, August 25, 2011

No Tablet For Me
… yet


I don't have a tablet. They all look really, really cool when you see them, and they're great fun to play with: you can spend hours finger drawing, playing games, flipping through a book, surfing the web…

Then reality sets in: I don't need one. I've got a compact, light laptop with a keyboard. I've got an Android smartphone that lets me check email, surf the web and fits in my pocket. There are few situations where a tablet could realistically replace either.

A tablet doesn't fit in your pocket. You need a bag — and if you have a bag then you can bring a laptop. The laptop is vastly faster, with way more memory and storage. A larger screen, a real keyboard and a full operating system that lets me do long-form writing, software development and data analysis among many other things. A tablet isn't a replacement for a laptop and won't be for many years, if ever.

Unlike a tablet my smartphone will go in my pocket and still does most things a tablet could: surf the web and do email, read books, play games and so on. And it's also my phone; it comes along whether I bring anything else or not. A tablet isn't a replacement for my phone either.

I'm not alone it seems. I see plenty of notebooks, and everyone and their dog carries a phone. But for all the hype, I see precious few tablets out in the wild. A tablet is still a rarity during my commute. I have only seen half a dozen people in total trying to use them for serious work - showing presentation slides, taking notes, drawing illustrations during a discussion, that sort of thing. I don't think I've seen anyone do it twice. It really is mostly a toy, not a serious tool.

But for a toy they tend to be heavy and expensive. Many tablets are the size and weight of a large hard-cover book — too heavy to hold in your hands for very long, and large enough to be jostled and bumped in a crowded train. The purchase price is high and the monthly contract — usually required — on current tablets is almost as much as I pay for my phone subscription. Fine for a tool, but it's too much money for a toy.

But — what if it was so cheap you could buy one on a whim? What if it didn't need a monthly subscription? What if it was so small and light that you could actually use it as a decent text reader?It'd still be a toy of course, but an affordable one, and one with an actual use.

As it happens, there's a very interesting tablet just about to be announced. the Andy Pad Pro is a British-made1 7-inch — about 9x15 cm — Android tablet with good specifications and a seriously low price. It's fairly fast with a higher-end ARM cpu and 3d graphics hardware, a decent amount of memory and storage and a 1024x600 pixel capacitive touch screen. There's a standard(!) USB port and a HDMI port for full HD video output, and both front- and back-facing cameras. Good specifications, far better than budget tablets. It should let me run any application, read PDFs and books, and play any kind of game.

Apart from the specs, there's a few things that set this one apart: First, it's open. The system is unlocked, so you can replace the supplied Android 2.3 with another version or another OS if you want. And they hope to update it to "Ice Cream Sandwich" — the next version of Android — once it's publicly available. The company has been really responsive when I've emailed them, and I hope and expect they will continue to be responsive and open in the future too. I'd love to see some documentation on the hardware and drivers on the website for instance.

Second, the price is good. At £179, about 21000 yen, it's cheap enough that I can get one just for fun. At that price, and being open, I can find good use for it no matter what. If I end up not using it as a tablet, I could try running another kind of Linux on it; use as screen and controller for some project (could make a great replacement server for my homebuilt temperature logger - and its little brother is almost so cheap you could get one just for that); or simply use as a development target when I get the urge to develop for Android again.

Oh, and third: it looks nothing like the glass-and-aluminium tablets that's all the rage right now. It doesn't copy anyone else, but has a simple and straightforward design that's quite appealing to me; I can carry this around without a feeling that I should wear a turtleneck sweater, hornrimmed glasses and an arrogant sneer. And I'd be far less worried about dropping this than dropping one of those easily scratched tablets with exposed glass corners.

On the down side there is no mobile connectivity, only Wifi. The battery life will probably be a bit limited, and the screen is unlikely to be as bright and contrasty as more expensive units. The developers have surely cut corners elsewhere too. That's fine; I don't expect to get 50k yen worth of hardware for less than half the price.

I'm ordering one next week, and I'll be back with my impressions once I've used it for a while. Hopefully I'll receive it before we leave for Sweden later next month; a week-long trip should be a good test.

#1 Let's hold off on the "But does it leak oil?" jokes. It's the birth country of the ZX81 among many other iconic microcomputers after all. The ARM processor family — at the heart of almost all smartphones, tablets and netbooks among many other items — is developed in Britain too. The British computer industry never died; it just became embedded.

Tuesday, August 23, 2011

Short Answers to Complicated Questions

Question:     Japanese governments are typically weak, squeezed as they are between internal party politics — politicians are less loyal toward their parties than to their factions and money donors — industry associations and special interest groups, and a powerful, unaccountable bureaucracy that ignores the government at will. We've had five Prime ministers in as many years.

The current situation is even worse than usual. The ruling party is close to splitting over internal disagreements. The opposition has control of the upper house and is opposing any and all legislation it can in a bid to force the government to call a general election. A general election that won't be held any time soon: the DPJ knows it will lose many seats and wants to delay as long as possible; the tsunami-ravaged areas are still in no condition to hold any kind of election; and the supreme court has declared the current election district system unconstitutional.

Prime minister Kan has promised the opposition to resign in exchange for the passage of a few budget- and energy-related bills. This will happen within a couple of weeks, and the internal DPJ campaign for electing the next PM is in full swing; Maehara, Noda, Mabuchi and others are all possible candidates. This is just a temporary appointment, though, as the regular party leadership election is scheduled in a year.

The newly appointed PM will have virtually no political leverage with the opposition or the ministries and can count on no public support. Everyone knows they will face a re-election (and likely defeat) in a year, making them a lame duck from day one. The pressing problems — reconstruction of Tohoku, resolution of the Fukushima disaster, rapidly worsening state finances and the effects of a strong yen and worldwide recession — are all mostly out of their hands, but still their public responsibility.

Given the grave situation above, what practical effect will the choice of new Prime minister have on Japanese politics in general; and the task of rebuilding northern Japan, turning around the economy and formulating a new energy policy in particular?

Answer:     None.

Thank you for reading this edition of "Short Answers to Complicated Questions". Please join us again for the next edition where we tackle the complicated question of reality-based evidence for a supernatural origin of the universe.

Monday, August 22, 2011

Reality Isn't Anybody's Bitch
— Threats and the Need for Pseudonyms


Why would you want to have a pseudonymous identity online? How about this reason: you and your family get threats from chronic fatigue syndrome sufferers because you show that it isn't caused by a virus. Same thing happens to researchers that show that the link between autism and vaccines is false1. Same thing happens to climate researchers that show warming is, in fact, happening and is, in fact, caused by human activity. Geologists, palaeontologists and archaeologists that publish research contradicting some religion or another. Physicians that provide abortions, contraceptives or even just medical reproductive advice to women.

People that get targeted in this way can't have a normal online life. If you ask them to use their real names online, they will get tracked, harassed and shouted down whatever they try to do. Their families, friends and anybody in public contact with them put themselves at risk for the same kind of harassment. And while most threats are idle, a few are serious enough; researchers and their family members do get injured and killed in attacks.

But even idle threats and harassment is a serious thing to those who get targeted. More and more, our public discourse is online. If you get shouted down, if you get chased out of that discourse, your right to participate — and our democratic systems are built on people having that right and using it — is compromised, and your viewpoint goes unheard. Googles shortsighted "real name" policy is ultimately very damaging, to Google itself, but also in a small way to the greater society.
Real names don't stop this harassment. Most people harassing scientists already do so openly, under their own name, proudly brandishing their membership in whatever cult or organization tells them to go ahead. Real names forces away the victims, not the attackers. Real names don't stop mob rule; it legitimises it.

But why are scientists targeted? This is not some temporary phase, and it's nothing new. It is because reality always wins.

You can't wish away reality. You can't ultimately ignore it. You can't bribe it off, reason with it or make a deal with it. You can curse it; condemn it as immoral and evil; you can make it illegal — but reality just Will. Not. Care. If your ideology or religion contradicts reality, well so much the worse for you and your ideas. Reality won't shift just to accommodate you.

We all live with a complicated structure of ideas, assumptions, prejudices, ideologies and notions of how the world around us ought to be. We are not likely to like people that come along and show that bits of that structure is wrong or even harmful.

The Chronic Fatigue sufferers wanted a cause — any cause — for their condition, even if it doesn't lead to a cure. A few no doubt want it to be a physical cause; mental conditions are still heavily stigmatized and it becomes so much easier to bear when you can point to something physical. A chronic virus infection is a great explanation. It fits a lot of the data and you finally get some kind of target; it points to things you can try and ways to alleviate symptoms, but most of all it gives you a coherent reason. We humans love to have reasons for things.

Then a bunch of researchers comes along and shows the data was wrong — there is no virus and we still have no clue. Some of the patients feel it really would have been better to leave things alone; a comforting lie is easier to live with than a disagreeable truth. Getting hope, then having it yanked away from you breeds a lot of resentment, denial and even, in a few already unstable individuals, threats of violence. And since reality is inviolate that anger, resentment and violence gets directed at the messenger instead.

People realize their cherished ideas are safe only as long as nobody shows they contradict reality. So the only way to keep their ideas safe is to drive out, shout down and silence those that would expose facts that contradict them.

This, I suspect, will become more and more common, and spread to more fields over time. There is hardly a field of research that doesn't contradict some dearly held beliefs of people somewhere. Through the internet those believers can now easily find each other — and find researchers that publish contradictory findings. It's much easier to disrupt somebody's online presence than their real life. At the same time, your online life is rapidly moving from an idle hobby to an important part of your core life.

I write very little about my work online as it is. If I were in any kind of sensitive field, I doubt I would write anything science-related under my own name at all.

#1 And in that case, the initial claim was deliberate paid-for fraud on the part of Andrew Wakefield, committed in order to bolster legal malpractice cases and to give a market opening to his own, alternative vaccine.

Thursday, August 18, 2011


I've been on Google+ for a few weeks now. It's another "social network" like Facebook, Mixi, Twitter, LinkedIn and so on; a place to connect with people and follow them. It's still invitation only (though see below) but it's surprisingly useful already; there's plenty of interesting people1, and some friends and acquaintances of mine are already active there as well.

You add people to follow them. Unlike Facebook, but like Twitter, you can add somebody to see what they're saying without them having to add you back. Many of our relationships are not symmetrical, and G+ recognizes that.

Unlike Twitter you're not limited to 140 characters of text. Your posts can be as long as you want (though it tends to favour shorter posts), and you can add links, pictures and video right in your posts. And people can comment directly in each post so the conversation becomes much easier to follow.

And G+ is different from both Facebook and Twitter in that you're in control. You can easily, naturally decide who can see what you write, and you decide whose posts you want to see in turn. Your friends won't see work-related posts, and your boss won't see any embarrassing party pictures or posts about your vacation. And nobody can spam you with posts you don't want to see.

Tai Kamaboko

G+ does this with circles. You add people to one or more circles, or groups of people. You can have as many or as few circles as you want — you can have just a single circle with everybody in it if you don't want to bother. People know if you add them, but they don't know to what circles. You could put them in "Best Friends Forever!!!" or in "Crushing Bores" and they'll have no idea.

You choose what circles can see each post. I have a circle for my Swedish-speaking contacts , for instance, where I can post in Swedish without bothering anyone who can't understand it. I have another circle for Japanese, a circle for other scientists and so on. You could have a circle for co-workers to post internal work matters in private, a circle for family members or whatever. You can easily put people in more than one circle — my brother is in both my Family circle and Swedish circle for instance.

These circles also determine whose posts you see. Your stream of updates will only show posts from people that you have added. Nobody can add you to one of their circles to spam you with messages you don't want. If somebody adds you it just means you could see their posts. You won't actually see them unless you add them in turn.

You can choose to post "Public" instead of to particular circles. Anybody who has added you will see those posts, and they will also show up on your front page. If you go to my page and you aren't a member, or I haven't added you, then what you see are my public posts. It's like a blog post or a Twitter update. On the other hand you can post to just a single person; that would be much like a private email.
Midōsuji Line, Shinsaibashi

There's group chat and there's a nifty-looking group video phone which I haven't really tried as I have neither webcam nor headset — though my brother did show me my new niece through his webcam so I know it works. It seems to be really useful for quick meetings or family calls. There are no "brand" or company pages yet — not a bad thing — and no advertising. That will no doubt change eventually. Games have recently been added, but mercifully they've kept on a separate page so you won't see any posts at all about them unless you choose to go there.

Google has decided to disallow openly pseudonymous accounts. This is a serious mistake, I think; there's several important, ethical reasons2 not to use your off-line name in online forums. They allow celebrities to use pseudonyms rather than real names ("Lady Gaga" is there, not "Stephanie Germanotta"), and real-sounding names go unchallenged unless someone reports them. I hope they'll see sense and revisit and change this at some point, perhaps once they allow brand names and company accounts.

It looks good so far. It's still partially unfinished, there's some rough spots, and the misguided "real name" policy is a cause for worry. But if they manage to steer clear of any major mistakes this looks like a real winner. If you want an account, all you need to do is to follow this link: Google+ invitation.

#1 With Linus Torvalds on one hand and Paris Hilton on the other, you're spanning a fair chunk of the industrialized world already.

#2 A couple of examples:

- You're a woman harassed by an abusive ex-husband, and want to participate online without him finding you.

- You have a position of some authority — a teacher, say — and want to participate in political or religious discussions without people accusing you of being partisan and trying to push your beliefs onto your students.

- You work with animal experiments or in an abortion clinic — or working against animal experimentation or abortion; you volunteer to help illegal immigrants; or any other sensitive or controversial field that you want to discuss but you don't want potentially unhinged people to easily find your family or friends.

- You are part of a despised minority or you've had a particular (perhaps psychiatric) disease, and you want to discuss this with others without potential employers or your family finding out about it.

- You simply want to hide your gender or your ethnic background in order to avoid the sleazeballs and racists that always crop up wherever you go online. Note that Google allows you to hide your gender in your profile page, but still require your real name, making it pretty pointless.

Tuesday, August 16, 2011

About the Blog, By The Way…

You may have noticed that I'm posting more lately than I used to. Our paper has been submitted, so I guess it's not soaking up all my writing energy any more, leaving more writing time for the blog. If that is the reason — and I have no reason to believe otherwise — it means I have some fixed amount of writing I want to or need to do every day, one way or another.

I wonder if the writing time I spend on other websites, on email, on paper reviews, on long-form homework and so on also counts? If so, I probably spend more time writing — in three languages no less — than I spend doing anything else at all in my life. And here I thought I'd left the liberal arts behind when I chose a science career…

Monday, August 15, 2011

It's The O-bon Holidays
- so what am I doing in this office?

It's O'bon, the yearly summer holiday where many people return to their hometowns to meet relatives, attend festivals and honour their ancestors. Many businesses are closed or working at reduced capacity. NAIST has most of the week off — not even the cafeteria is open — and plenty of people didn't show up last Friday either.

I have three days off too, but I've chosen not to use them now. Instead I'll take those three days toward the end of September. Together with a couple of national holidays it will give me over a week off, enough time that we can fly to Sweden to visit my parents and meet my new niece.

So I'm at work. Not quite alone but nearly so. On the upside it's quiet and relaxing, and there's no seminars or meetings or anything to distrupt you. Even the closed cafeteria has a silver lining: I brought oatmeal, milk and a banana for lunch instead of the usual cafeteria fare. Japanese aren't much for porridge in general so I rarely eat this at home, but now I get to indulge for a couple of days.


Time off or not it's still O-bon, though, and like previous years we're sun-drying our umeboshi. It's a good time for it; the weather is hot and sunny and there is less traffic on the streets.

Sunday, August 14, 2011

Cinnamon Rolls

It's Sunday, with nothing to do all day. What would be better than to bake cinnamon rolls? A mug of cocoa and a still-warm cinnamon roll is a rare treat.

Cinnamon Rolls

Cinnamon rolls, still warm from the oven.

Friday, August 12, 2011

A Day Without Power

High Power

Did a little laptop-battery experiment yesterday. My wonderful laptop lasts for a good, long while on battery, I know that. However, I've never found out exactly how long it lasts if I use it for my everyday work. More specifically, can I use it for an entire workday or not, using only the battery?

This matters. Say I get to work and the power adapter is gone or broken. Or I'm on a business trip and forget the adapter at the hotel. Or on a 12-hour flight to Europe. It'd be good to know exactly how much I can get done before the computer dies on me.

So yesterday morning I come to work and did not plug it in. The computer was sleeping during my commute so the battery was nearly but not quite full. To save power I did a few things: I turned down the screen brightness to a low but still comfortable level; turned off the wireless as I don't use it at work; and I put the computer to sleep whenever I was reading something for instance, or when I went to lunch.
I worked as usual: I'm making a few presentation slides and a list of talking points in Open Office; looked up some papers; read up on a communications library I'm trying to use; and the usual email, websurfing, Octave use, writing a blog post and so on. I did very little coding, and no image editing or anything like that.

I started right after 9 in the morning. When I left for home about 18:20 I had 15% charge left, which should realistically have lasted me about another half an hour to an hour if I needed it (a straight estimate is over an hour, but those last percentages aren't very reliable). Nine hours and a bit, and possibly up to ten hours if I push it.

So yes, I am able to do a whole day of light work without power. I could do a whole day of conferencing or a flight to Europe if I am careful, put it to sleep whenever I break and avoid using the wireless too much. I could not do it if I did mostly software development or image editing; both use the CPU and disk a lot and will drain the battery faster. Battery life is still not good enough — I'd want to be able to confidently leave the power brick at home over the day for that — but it's getting there.

Thursday, August 11, 2011

Amazon eBooks

So... Amazon ebooks. They have a reader application for my Android phone. And now they have an online reader that works fine under Ubuntu and Chromium. Thought I'd try buying and reading an ebook, just for the experience. It's The Wave Of The Future after all, and who wants to miss that?

I've never read the famous Stieg Larsson thriller trilogy, despite it being in my native language and all. It's the kind of stuff you'd read once then forget about — perfect for an an experiment like this. So I search for it, but alas, it's not available on the Amazon store at all; all I can find is the English translation.

Next try: I'm reading 火車 by Miyabe Miyuki. I have it on paper already so nothing lost if the experience is bad, and it could be really convenient to read Japanese on a device where I can directly look up kanji and words I don't know. But again, they seem to have none of her books in Japanese1.

Well, Amazon is based in a mostly English-speaking country. Better try something in that language. Fortunately, Charles Stross has just recently published his new novel, "Rule 34". Sure to be a good read if nothing else. And it is available — but for more money than the hardcover2. Um, no thanks. I prefer to pay less for the the extra value of a physical book if it's all the same. Or even better, I'll just wait for the paperback.
No ebook for me yet. I still want to try it, but it'll have to wait until I find something I want in a language they support, at a lower price than the paper book.

#1 or anything in Japanese at all, though I could be wrong there; a search for "日本語" ("Japanese") mostly gives me soft-core porn and no titles in Japanese.

#2 Yes there's shipping, but I'm ordering some other books on paper anyway so there extra cost for this one is zero.

Wednesday, August 10, 2011

World Press Photo 2011 this Weekend

A quick reminder for anyone in Osaka: the World Press Photo 2011 exhibition is this week, at Herbis in Umeda, until next Thursday. We'll be going this weekend. They show pretty much around the world, so check their website for schedule and locations.

This exhibition is a favourite of mine. Not all pictures are good, and some pictures can be disturbing — much like the news it covers — but it never fails to engage me. If you have the chance to catch it, do so.

Monday, August 8, 2011

Is Internet Destroying Your Brain!?
- hint: No, it's not.

Rewire Your Brain
For Fun And Profit!

Susan Greenfield, a supposedly actual scientist — somebody who really, really should know better — ignores any contrary evidence in order to push a scare about the internet destroying young people. She's the source of the idea that "The Internet is Rewiring our brains!!! (OMG! We're going to DIE!!!)".

Well, of course using the internet rewires our brains. Any experience rewires our brains — that's what brains do. When you remember something, that happens by the brain rewiring itself to add that memory. You can use the same argument for any experience: "Having sex rewires our brains!", "Having breakfast rewires our brains!", "Having fun rewires our brains!". Reading about Greeenfield certainly rewires my brain to become cranky and annoyed for hours afterwards.

She's been pretty thoroughly debunked, but lack of evidence doesn't seem to stop her in any way. She's apparently not happy with the waning press coverage however, so now she's claiming that the internet and social websites in particular is a cause of autism.
Several people such as Dorothy Bishop point out some obvious problems with that idea, such that a) the rise in autism diagnosis started long before the internet became a public medium; and b) autism is typically diagnosed at the age of two, long before children start using social sites. Her answer — her full scientific argument, really — is:
"I point to the increase in autism and I point to internet use. That's all."

Panasonic Let's Note S9
Apparatus Of
"That's all", and that's the problem. Carl Zimmer (read his blog; it's great) Have an excellent summary. And as he points out, some people have taken this brilliant piece of argumentative excellence and run with it on twitter. The result is pearls like:
"I point to Alzheimer's and I point to cheese doodles. That's all."

"I point to diabetes and I point to cats. That's all."

Take-away lesson: Somebody may have a "PhD" at the end of their name — or an "MD", or a "Rev.", or "Civ. Eng.", or anything — but that doesn't guarantee they're not ignorant about what they say, or that they're not trying to push an agenda they know to be false (if they're a "Rev." that's more likely than not of course).

Sometimes an expert in one field wades in to do cocksure pronouncements in another without understanding it, and end up embarrassed. "Expert" critics of global warming, for instance, tend to be engineers or physicists without a background in climatology. Engineers and physicians seem particularly prone to this. They have a method-based hands-on understanding of one particular subfield, and think they can apply their methods to other fields without learning enough background to actually understand it.
And we're all human. As much as we want scientists to be objective and disinterested, the reality is that we all have our biases and hobby-horses, and we're concerned about our own careers, our pensions and mortgages. We grow old and cranky and stop learning new things. We refuse to let go of favourite ideas long after they've been disproved. We may have religious or political biases that blinds us to some facts. Some may see fame and fortune — or at least a modest side income — from ignoring evidence and science in favour of publicity and a book deal.

I'm not arguing against expertise. An expert is a lot more knowledgeable than a non-expert and people know this — would you rather have a bypass operation done by a heart surgeon or by a plumber? But check that the expert really is an expert in that particular field; how about open heart surgery by a psychiatrist, a dermatologist or an eye surgeon? They're all MDs too after all.

Ask yourself if this person might have a bias or some reason to not be completely open and accurate. If they happen to run for office, or if they are devoutly religious they may have reason to make the science sound like what they or other people want to hear. If they're selling a book, or if they're paid by a particular interest group or company there's reason to be suspicious.

But most of all, if a claim is at all sensationalist or surprising, ask for the evidence. If they have evidence — if they have data and analysis, and if that has been corroborated by others — they should be happy to disclose it. If they show only sketchy, suspicious or discredited data, or if they show nothing at all, then that probably means they have no solid evidence. If so, ignore them. If they are right, then people will find good, solid evidence sooner or later. If not, then you won't have wasted your time, and possibly your health and your money, on a fraud.

Thursday, August 4, 2011

Rokko Mountain

We celebrated my birthday recently, and as usual we went out to eat together. A birthday is a good excuse to try something new, so we tend to pick some place we wouldn't normally go to. Beyond our normal budget, a kind of restaurant or food we wouldn't usually have, or perhaps at an interesting location.

Have A Seat

Mikage station on the Hanshin line. From here you take the bus to the Rokko ropeway base station where you go up the mountain. At the top you can take another bus or you walk to the hotel. Walking is more pleasant, but bring a change of clothes in the summer.

The dinner was late this year; I was still at OCNC in Okinawa on my birthday, and we delayed it another couple of weeks to let me catch up with things once I came back. But a few weeks ago we finally went to Rokko mountain in Kobe, and to the barbecue at Rokko Mountain Hotel.

Mountain Shop

There's no real town along the top ridge, just houses spread out along the road, but it does have this store with daily foods and a large selection of wines, beers and spirits, including a local Rokko beer. There's many summer homes and corporate retreats on the mountain, so I can see the demand.

We last went there for O-bon two years ago. We had the buffet, which was tasty, but of course still buffet-type food. At the time we decided to return some day and have the course menu instead. Expensive, but with higher-quality food. My birthday was a perfect opportunity.


The lobster, with scallops and squid gently frying in the background. Overdoing the depth of field thing here, I think.

The course menu was very good indeed. The appetizer was a sampling plate with sashimi, marinated seafood and vegetables. The small lobster cooked in its own shell was succulent, and the main course meats were tender and flavourful, and included various cuts of lamb, chicken, pork and beef as well as sausages and lots of vegetables. My favourite (if not Ritsukos) was the lambchops, but the beefsteak and the thick bacon slices were excellent too. It finished with dessert and coffe. Well worth trying as an experience. The weather was rather hazy, unfortunately, so the view wasn't very photogenic.


Hydrangea grow wild all over the mountain. They're not native to Japan so they're probably escapees from some garden long ago. At this time the whole mountain top is lit up in light blue flowers.

Tuesday, August 2, 2011

An Apology

I owe a lot of people here an apology.

Whenever somebody comments on the blog I get sent an email to my Gmail account. I love getting comments, and more often than not I try to answer. I thought there'd been very few comments lately, so I took a look ­— and there's lots of them. And I've missed them all.

What happens is, there's a lot of spam comments to this blog (to every blog, anywhere), and they get caught by Blogger before they're ever published. They still generate an email, though. And with all these spam emails showing up every day, lately Gmail has decided all email about comments on this blog is spam, and moved them directly to the spam folder.

I've missed almost all comments to this blog for the past month. I haven't ignored you, and they're deeply appreciated. I just completely missed them, due to my own inattentiveness. Again, I apologize. If there's anything you think I should answer then feel free to post it right here.

I Submit

I've been working on a paper off and on for most of this year, and last week we finally managed to submit it. Now we wait — we wait for the editors to decide if it's appropriate for the journal; we wait for them to send it out to reviewers; we wait for the reviewers to submit their reviews, and we wait for the editors to decide whether the paper has a chance of being accepted.

This can take anything from a month (that would be fast) to six months, though a year is not unheard of. I'd expect it to be three or four months. If they decide it can be accepted, we have to revise the manuscript according to the reviewers comments, or explain clearly why we think a suggested change is unnecessary or harmful. The revisions can range from spelling errors, up to redoing the whole model from the ground up, running new sets of simulations or completely change the way we analyse our data. Our changes may be submitted back to the reviewer for further comment if the editor thinks it's needed.

If the editor or reviewers think the paper is not acceptable, or if we don't think the required revisions fit the paper we want to publish, then we give up on that journal. We'll decide on a different journal, rewrite the paper to fit that journal, and submit it again. All in all, six months to a year from first submission to publication would be quite normal. Three months is fast; expect a year and a half to two years if you have to resubmit the paper.
All well and good — except that our project ends next March. We lose access to the cluster computer we've been using for our simulations, and I no longer have a job. We might come to the point where we're asked to do a new set of simulations for the paper and we simply can't: we no longer have the computing power, and I might not even have a science-related job any more so I may have little or no time to work on the model or the paper.

It won't come to that, hopefully. Even if the project ends, we could probably ask for a little computing time to finish the project. And if I find a research-related job it's accepted practice to spend some time finishing up things from your previous projects. Time will tell, as always.